The Y chromosome provides an unusual opportunity to examine population genetic processes like hitchhiking and background selection because of its recombinational isolation from other chromosomes, its effectively haploid transmission, and its restriction to males. Progress in studying Y chromosome population genetics of Drosophila has been held back by our ignorance of protein-coding genes and single-copy sequence. By using BLAST in the reverse of the normal approach, we have successfully identified eight new protein-coding genes on the Y chromosome of D. melanogaster. We are now in a position to provide a thorough quantification of patterns of variation on the Y chromosome of D. melanogaster, and to place this in the context of interspecific sequence divergence with related species. Four competing models, not all mutually exclusive, make predictions about levels of variation on a Y chromosome. They are Muller's ratchet, background selection, the Hill-Robertson effect, and hitchhiking. All four lead to the prediction that standing levels of variation on the Y ought to be depressed compared to autosomes, but they make different claims about the frequency spectrum, degree of population subdivision, and age distribution of alleles. We propose to parameterize and to quantitatively weigh the merits of these competing hypotheses through the following three aims: First, we will quantify and model intraspecific polymorphism in protein-coding genes on the Y chromosome of D. melanogaster by a combination of dHPLC and direct sequencing of Y-linked protein-coding genes in a set of 96 Y chromosome replacement lines of global distribution. Second, we will obtain corresponding sequences from a series of related species, in order to determine divergence rates and to characterize the molecular evolution of intronic Y heterochromatin. Finally, we will test associations between segregating Y variation and variation in sperm function through sperm kinematics assays and tests of sperm competitive ability. These studies will establish D. melanogaster as a key experimental system for analysis of Y chromosome polymorphism and molecular evolution.